Abstract
The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X-ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described.
Highlights
The Protein Data Bank in Europe (PDBe; http://pdbe.org; Velankar et al, 2010, 2011), previously known as the European Macromolecular Structure Database (MSD; Velankar et al, 2005; Tagari et al, 2006), is the European partner in the Worldwide Protein Data Bank
The master copy of the PDB resides on an ftp server hosted by RCSB, with mirrors at PDBe and PDBj
The wwPDB partners collaborate intensely on all matters related to ‘data-in’; that is, the deposition and annotation of structures and data and issues related to formats, standards, validation and the description of the ligands that occur in the PDB
Summary
The Protein Data Bank in Europe (PDBe; http://pdbe.org; Velankar et al, 2010, 2011), previously known as the European Macromolecular Structure Database (MSD; Velankar et al, 2005; Tagari et al, 2006), is the European partner in the Worldwide Protein Data Bank (wwPDB; http:// wwpdb.org; Berman et al, 2007). Together with its wwPDB partners, RCSB (Kouranov et al, 2006), PDBj (Standley et al, 2008) and BMRB (Ulrich et al, 2008), PDBe accepts depositions of experimentally determined biomacromolecular structures and the underlying experimental data. The deposition sites curate (i.e. annotate, enrich and validate) the structures and the data and make them available in the Protein Data Bank (PDB; Bernstein et al, 1977; Berman, 2008). The wwPDB partners collaborate intensely on all matters related to ‘data-in’; that is, the deposition and annotation of structures and data and issues related to formats, standards, validation and the description of the ligands that occur in the PDB.
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